Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

RGAP (Rice Genome Annotation Project)

General information

Description: We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species.
Year founded: 2005
Last update: 2013
Version: Release 7
Accessibility:
Manual:
Accessible
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Country/Region: United States
Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: The Institute for Genomic Research
Address: The Institute for Genomic Research, Rockville, Maryland 20850, USA.
City: Rockville
Province/State: Maryland
Country/Region: United States
Contact name (PI/Team): MSU Rice Genome Annotation Project Team
Contact email (PI/Helpdesk): rice@plantbiology.msu.edu

Record metadata

Created on: 2018-01-27
Curated by:
Qi Wang [2018-02-14]
Dong Zou [2018-02-07]
Tongkun Guo [2018-01-26]

Ranking

All databases:
180/4549 (96.065%)
Gene genome and annotation:
76/1211 (93.807%)
Metadata:
10/436 (97.936%)
180
Total Rank
660
Citations
44
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Publications

17145706
The TIGR Rice Genome Annotation Resource: improvements and new features. [PMID: 17145706]
Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR.

In The Institute for Genomic Research Rice Genome Annotation project (http://rice.tigr.org), we have continued to update the rice genome sequence with new data and improve the quality of the annotation. In our current release of annotation (Release 4.0; January 12, 2006), we have identified 42,653 non-transposable element-related genes encoding 49,472 gene models as a result of the detection of alternative splicing. We have refined our identification methods for transposable element-related genes resulting in 13,237 genes that are related to transposable elements. Through incorporation of multiple transcript and proteomic expression data sets, we have been able to annotate 24 799 genes (31,739 gene models), representing approximately 50% of the total gene models, as expressed in the rice genome. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 59 tracks. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads.

Nucleic Acids Res. 2007:35(Database issue) | 531 Citations (from Europe PMC, 2020-02-08)
15888674
The institute for genomic research Osa1 rice genome annotation database. [PMID: 15888674]
Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, Lin H, Hamilton J, Haas B, Sultana R, Cheung F, Wortman J, Buell CR.

We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species. Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules, or virtual contigs, of the 12 rice chromosomes were constructed. Our most recent release, version 3, represents our third build of the pseudomolecules and is composed of 98% finished sequence. Genes were identified using a series of computational methods developed for Arabidopsis (Arabidopsis thaliana) that were modified for use with the rice genome. In release 3 of our annotation, we identified 57,915 genes, of which 14,196 are related to transposable elements. Of these 43,719 non-transposable element-related genes, 18,545 (42.4%) were annotated with a putative function, 5,777 (13.2%) were annotated as encoding an expressed protein with no known function, and the remaining 19,397 (44.4%) were annotated as encoding a hypothetical protein. Multiple splice forms (5,873) were detected for 2,538 genes, resulting in a total of 61,250 gene models in the rice genome. We incorporated experimental evidence into 18,252 gene models to improve the quality of the structural annotation. A series of functional data types has been annotated for the rice genome that includes alignment with genetic markers, assignment of gene ontologies, identification of flanking sequence tags, alignment with homologs from related species, and syntenic mapping with other cereal species. All structural and functional annotation data are available through interactive search and display windows as well as through download of flat files. To integrate the data with other genome projects, the annotation data are available through a Distributed Annotation System and a Genome Browser. All data can be obtained through the project Web pages at http://rice.tigr.org.

Plant Physiol. 2005:138(1) | 129 Citations (from Europe PMC, 2020-02-08)